[Freesurfer] Creation of V1 mask in volume

[Florence Campana]

Dear freesurfer experts,

I am trying to create a V1 mask in volume, based on the V1 label, in
fsaverage space.


I use the following command: mri_label2vol --label
/Applications/freesurfer/subjects/fsaverage/label/rh.V1.label --temp
/Applications/freesurfer/subjects/fsaverage/mri/orig.mgz --hemi rh
--identity --o v1volume.nii

When I check out the output (in freeview, I load orig,mgz and v1volume.nii
as a mask), V1 as defined in v1volume.nii  seems to be mislocated. I am
surprised  since I would think that I use the proper inputs ; or is my
command line somehow wrong?

Thank you very much,
Florence
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Re: [Freesurfer] Problem flipping a label into other hemisphere

[Neuro Lists]

Hi,
The one I tested with in the last couple of messages is just the standard
bert subject after having done:

cd ${SUBJECTS_DIR}/bert
cd surf
mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right
rh.sphere.left_right

And then running:

cd ../label
mris_apply_reg --src-label lh.BA45.label --trg lh_flip.BA45.label --streg
../surf/lh.sphere.left_right ../surf/rh.sphere.left_right

Have I misunderstood something?

Thanks again!

On Tue, Oct 17, 2017 at 4:55 PM, Douglas N Greve 
wrote:

> Is this fsaverage or one of your own subjects?
>
>
>
> On 10/17/2017 02:18 PM, Neuro Lists wrote:
> > Hi Doug,
> > Thanks a lot for looking into it. Unfortunately it's still not working
> > though.
> >
> > See here:
> > https://imgur.com/a/lxXUH
> >
> > Thanks again!
> >
> > On Mon, Oct 16, 2017 at 12:31 PM, Douglas Greve
> > > wrote:
> >
> > Sorry, try this
> >
> > mris_apply_reg --src-label lh.BA45.label --trg lh_flip.BA45.label
> > --streg ../surf/lh.sphere.left_right ../surf/rh.sphere.left_right
> >
> >
> > On 10/13/17 2:58 PM, Neuro Lists wrote:
> >> Hi all,
> >> I was just wondering if there was any further insight into what I
> >> might be doing wrong on this.
> >>
> >> Thanks again!
> >>
> >>
> >>
> >> On Thu, Oct 12, 2017 at 10:30 AM, Neuro Lists
> >>  >> > wrote:
> >>
> >> Hi Doug and Bruce,
> >> I forgot to mention that I had tried that as well but without
> >> success. As a sanity check, tried flipping a label from the
> >> 'bert' subject and it still comes out wrong. I've uploaded a
> >> screen shot of the result:
> >>
> >> https://imgur.com/a/J6Phx
> >>
> >> Thank you for any input you might have!
> >>
> >> These were the exact steps the following (I also tried
> >> playing around with the options to --streg but without luck):
> >>
> >> cd ${SUBJECTS_DIR}/bert
> >> cd surf
> >> mris_left_right_register lh.sphere rh.sphere
> >> lh.sphere.left_right rh.sphere.left_right
> >> cd ../label
> >>
> >> mris_apply_reg --src-label lh.BA45.label --trg
> >> lh_flip.BA45.label --streg ../surf/lh.sphere.left_right
> >> ../surf/rh.sphere
> >>
> >>
> >> $Id: mris_apply_reg.c,v 1.9 2016/12/06 19:40:48 greve Exp $
> >>
> >> cwd /home/joe/subjects/bert/label
> >>
> >> cmdline ../../scripts/mris_apply_reg --src-label
> >> lh.BA45.label --trg lh_flip.BA45.label --streg
> >> ../surf/lh.sphere.left_right ../surf/rh.sphere
> >>
> >> sysname  Linux
> >>
> >> hostname computer
> >>
> >> machine  x86_64
> >>
> >> user joe
> >>
> >> srcvalfile  (null)
> >>
> >> trgvalfile lh_flip.BA45.label
> >>
> >> nsurfs  2
> >>
> >> jac  0
> >>
> >> revmap  0
> >>
> >> 1 Loading ../surf/lh.sphere.left_right
> >>
> >> 2 Loading ../surf/rh.sphere
> >>
> >> Loading label lh.BA45.label
> >>
> >>4060 points in input label
> >>
> >> MRISapplyReg: nsurfs = 2, revmap=0, jac=0,  hash=1
> >>
> >> MRISapplyReg: building hash tables (res=16).
> >>
> >> MRISapplyReg: Forward Loop (133299)
> >>
> >> MRISapplyReg: Dividing by number of hits (133299)
> >>
> >> MRISapplyReg: nSrcLost = 38462
> >>
> >>4505 points in output label
> >>
> >> mris_apply_reg done
> >>
> >>
> >>
> >>
> >>
> >>
> >> On Thu, Oct 12, 2017 at 5:06 AM, Douglas Greve
> >>  >> > wrote:
> >>
> >> Try
> >>
> >> mris_apply_reg --src-label your.lh.label --trg
> >> your.rh.label  -streg lh.sphere.left_right rh.sphere
> >>
> >>
> >> On 10/11/17 5:43 PM, Neuro Lists wrote:
> >>> Hi all,
> >>> I've searched the lists extensively and have not been
> >>> able to resolve my problem. I'd greatly appreciated any
> >>> help.
> >>>
> >>> I have run the recon-all pipeline on a number of
> >>> subjects, made the appropriate fixes and am happy with
> >>> the surfaces. For each subject, I have a number of ROIs
> >>> that are created programmatically and they are exactly
> >>> as they should be. These ROIs are on the "regular"
> >>> surfaces, not the inflated ones. In other words, opening
> >>> the brainmask.mgz in freeview and just loading the label
> >>> file results in the ROI being where I expect it to be.
> >>>
> >>>
> >>>  I'm now trying to flip the ROI onto the contralateral
> >>> hemisphere and this is going terribly wrong. No matter
> >>> what I 

Re: [Freesurfer] Problem flipping a label into other hemisphere

[Douglas N Greve]

Is this fsaverage or one of your own subjects?



On 10/17/2017 02:18 PM, Neuro Lists wrote:
> Hi Doug,
> Thanks a lot for looking into it. Unfortunately it's still not working 
> though.
>
> See here:
> https://imgur.com/a/lxXUH
>
> Thanks again!
>
> On Mon, Oct 16, 2017 at 12:31 PM, Douglas Greve 
> > wrote:
>
> Sorry, try this
>
> mris_apply_reg --src-label lh.BA45.label --trg lh_flip.BA45.label
> --streg ../surf/lh.sphere.left_right ../surf/rh.sphere.left_right
>
>
> On 10/13/17 2:58 PM, Neuro Lists wrote:
>> Hi all,
>> I was just wondering if there was any further insight into what I
>> might be doing wrong on this.
>>
>> Thanks again!
>>
>>
>>
>> On Thu, Oct 12, 2017 at 10:30 AM, Neuro Lists
>> > > wrote:
>>
>> Hi Doug and Bruce,
>> I forgot to mention that I had tried that as well but without
>> success. As a sanity check, tried flipping a label from the
>> 'bert' subject and it still comes out wrong. I've uploaded a
>> screen shot of the result:
>>
>> https://imgur.com/a/J6Phx
>>
>> Thank you for any input you might have!
>>
>> These were the exact steps the following (I also tried
>> playing around with the options to --streg but without luck):
>>
>> cd ${SUBJECTS_DIR}/bert
>> cd surf
>> mris_left_right_register lh.sphere rh.sphere
>> lh.sphere.left_right rh.sphere.left_right
>> cd ../label
>>
>> mris_apply_reg --src-label lh.BA45.label --trg
>> lh_flip.BA45.label --streg ../surf/lh.sphere.left_right
>> ../surf/rh.sphere
>>
>>
>> $Id: mris_apply_reg.c,v 1.9 2016/12/06 19:40:48 greve Exp $
>>
>> cwd /home/joe/subjects/bert/label
>>
>> cmdline ../../scripts/mris_apply_reg --src-label
>> lh.BA45.label --trg lh_flip.BA45.label --streg
>> ../surf/lh.sphere.left_right ../surf/rh.sphere
>>
>> sysname  Linux
>>
>> hostname computer
>>
>> machine  x86_64
>>
>> user     joe
>>
>> srcvalfile  (null)
>>
>> trgvalfile lh_flip.BA45.label
>>
>> nsurfs  2
>>
>> jac  0
>>
>> revmap  0
>>
>> 1 Loading ../surf/lh.sphere.left_right
>>
>> 2 Loading ../surf/rh.sphere
>>
>> Loading label lh.BA45.label
>>
>>    4060 points in input label
>>
>> MRISapplyReg: nsurfs = 2, revmap=0, jac=0,  hash=1
>>
>> MRISapplyReg: building hash tables (res=16).
>>
>> MRISapplyReg: Forward Loop (133299)
>>
>> MRISapplyReg: Dividing by number of hits (133299)
>>
>> MRISapplyReg: nSrcLost = 38462
>>
>>    4505 points in output label
>>
>> mris_apply_reg done
>>
>>
>>
>>
>>
>>
>> On Thu, Oct 12, 2017 at 5:06 AM, Douglas Greve
>> > > wrote:
>>
>> Try
>>
>> mris_apply_reg --src-label your.lh.label --trg
>> your.rh.label  -streg lh.sphere.left_right rh.sphere
>>
>>
>> On 10/11/17 5:43 PM, Neuro Lists wrote:
>>> Hi all,
>>> I've searched the lists extensively and have not been
>>> able to resolve my problem. I'd greatly appreciated any
>>> help.
>>>
>>> I have run the recon-all pipeline on a number of
>>> subjects, made the appropriate fixes and am happy with
>>> the surfaces. For each subject, I have a number of ROIs
>>> that are created programmatically and they are exactly
>>> as they should be. These ROIs are on the "regular"
>>> surfaces, not the inflated ones. In other words, opening
>>> the brainmask.mgz in freeview and just loading the label
>>> file results in the ROI being where I expect it to be.
>>>
>>>
>>>  I'm now trying to flip the ROI onto the contralateral
>>> hemisphere and this is going terribly wrong. No matter
>>> what I try, the ROI ends up being generated far outside
>>> of the brain.
>>>
>>>
>>> I was originally trying to use the xhemi pipeline, but
>>> then I realized from the forums that I could just
>>> use mris_left_right_register.
>>>
>>> I've done:
>>>
>>> cd subject/surf
>>> mris_left_right_register lh.sphere rh.sphere
>>> lh.sphere.left_right rh.sphere.left_right
>>>
>>> I've then tried using a number of varieties of
>>> mri_apply_reg that have been listed on the forum:
>>> 1) mris_apply_reg --src-label your.lh.label --trg
>>> your.rh.label  -streg lh.sphere lh.sphere.left_right
>>> 2) mris_apply_reg --src-label lh.source.label --streg
>>> 

[Freesurfer] Advice on covariates in qdec or mri_glmfit

[Jeff Crawford]

Hello everyone. I am having trouble understanding the statistical effects of a 
covariate versus a nuisance factor in freesurfer and I would appreciate some 
advice.

I want to run a correlation between cortical volume and the measurement of an 
enzyme while covarying for ETICV.

In qdec, I select volume as the measure, set the enzyme as a covariate, and 
select ETICV as a nuisance factor.

This works fine, however, I want to also control for the difference in using 
two separate scanners.
This would be a categorical variable and I understand that Freesurfer does not 
allow categorical variables to be nuisance variables.
The solution I found to this problem from two separate emails is that you 
either use the Manuel stream of mri_glmfit or use set scanner as a fixed 
factor, which produces a description of:

"Does the correlation between volume and enzyme, accounting for scanner, differ 
from zero? Nuisance factors: ETicV"

This sounds right to me, but I am confused as to the difference between 
"accounting for scanner" and "Nuisance factors: ETicV", when I thought they 
were the same thing.

Am I approaching this right? Do I need to use mri_glmfit to properly control 
for scanner? If so, then how would I specify a nuisance variable in a contrast?


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[Freesurfer] Yeo atlas FreeSurfer

[Martin Juneja]

Hi experts,

I am using Yeo atlas (7 networks) in my analysis. Where can I find name of
all the regions involved in each of these 7 networks in Yeo atlas?

Thanks.
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] Skull-stripped data submitted on FreeSurfer version 6.0.0

[Duran, Tugce]

I think that is the issue. Freesurfer thinks there is brainstem in the 
skull-stripped image. That’s why it labels whatever gray matter it sees as 
brain stem. 
We’ll add the brain stem to the data and run it like that. 

Thanks!
Tugce
 

On 10/17/17, 1:28 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Douglas N Greve"  wrote:

Copy it before you run recon-all and copy it to brainmask.mgz (not to 
auto). If there is no brainstem, then I think it will fail


On 10/17/2017 12:55 PM, Duran, Tugce wrote:
> Do you mean after –autorecon1 –noskullstrip done we copy T1.mgz to 
brainmask.auto.mgz and a link from brainmask.auto.mgz to brainmask.mgz? Because 
I also did that and saw some cerebral cortex labeled as brain stem. There is no 
brain-stem in my skull-stripped data.
>
> Tugce
>
>
> dur...@iupui.edu
>
> On 10/17/17, 12:39 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf 
of Douglas N Greve"  wrote:
>
>  No, but I think if you copy it to brainmask.mgz that it will then 
use that
>  
>  
>  On 10/17/2017 12:28 PM, Duran, Tugce wrote:
>  > Is there a flag like –noskullstrip where we can skip brain-stem 
parcellation/labeling?
>  >
>  > Tugce
>  >
>  > On 10/17/17, 12:07 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on 
behalf of Douglas N Greve"  wrote:
>  >
>  >  if they look ok, then I think they are ok
>  >
>  >
>  >  On 10/17/2017 12:05 PM, Duran, Tugce wrote:
>  >  > That is exaclty right! But how did freesurfer respond to 
that, performing the skull stripping to skull-stripped data?
>  >  >   Should I trust the results since they looked okay?
>  >  >
>  >  > Tugce
>  >  >
>  >  >
>  >  > dur...@iupui.edu
>  >  >
>  >  > On 10/17/17, 12:00 PM, 
"freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve" 
 
wrote:
>  >  >
>  >  >  if you put -all AFTER the -noskullstrip, then it would 
have performed
>  >  >  the skull stripping
>  >  >
>  >  >
>  >  >  On 10/17/2017 10:44 AM, Duran, Tugce wrote:
>  >  >  >
>  >  >  > Dear FreeSurfer Team,
>  >  >  >
>  >  >  > I have recently submitted my skull-stripped data 
into FreeSurfer v6.
>  >  >  > Since this is a separate process than the default 
recon-all –all, I
>  >  >  > followed the recommended steps that are posted on 
the FSwiki website,
>  >  >  > here is the link for it:
>  >  >  > 
https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.Ihavealreadyskull-strippeddata.CanIsubmitittorecon-all.3F
>  >  >  >
>  >  >  > By doing so, I accidentally submitted my data both 
with *recon-all
>  >  >  > -autorecon1 -noskullstrip -s  *and *–all 
*flag at the beginning.
>  >  >  >
>  >  >  > Using PBS script, here is an example of this:
>  >  >  >
>  >  >  > list="E001_V1 E002_V1 E003_V1 E004_V1 E005_V1 
E006_V1 E008_V1 E010_V1
>  >  >  > E011_V1 E013_V1 E014_V1 E015_V1"
>  >  >  >
>  >  >  > echo $list
>  >  >  >
>  >  >  > OUTDIR="/pathtodirectory/logs_KT"
>  >  >  >
>  >  >  > PREFIX="recon-all"
>  >  >  >
>  >  >  > for index in $list; do
>  >  >  >
>  >  >  > recon-all *–autorecon1 –noskullstrip*-i
>  >  >  > /pathtodirectory/$index/"$index".nii -subject $index 
-sd
>  >  >  > /pathtodirectory *-all *1>$OUTDIR/$PREFIX.$index.out
>  >  >  > 2>$OUTDIR/$PREFIX.$index.err &
>  >  >  >
>  >  >  > done
>  >  >  >
>  >  >  > wait
>  >  >  >
>  >  >  > I forgot to remove the flag –all at the end of this 
command.
>  >  >  > Therefore, freesurfer v6 processed my data all the 
way till the end
>  >  >  > and Viola it worked! And I am wondering If I could 
trust this data
>  >  >  > since it looks OKAY when I look at the segmentation, 
parcellation. Can
>  >  >  > I trust this skull-stripped processes data with 
–autorecon1
>  >  >  > 

Re: [Freesurfer] Problem flipping a label into other hemisphere

[Neuro Lists]

Hi Doug,
Thanks a lot for looking into it. Unfortunately it's still not working
though.

See here:
https://imgur.com/a/lxXUH

Thanks again!

On Mon, Oct 16, 2017 at 12:31 PM, Douglas Greve 
wrote:

> Sorry, try this
>
> mris_apply_reg --src-label lh.BA45.label --trg lh_flip.BA45.label --streg
> ../surf/lh.sphere.left_right ../surf/rh.sphere.left_right
>
> On 10/13/17 2:58 PM, Neuro Lists wrote:
>
> Hi all,
> I was just wondering if there was any further insight into what I might be
> doing wrong on this.
>
> Thanks again!
>
>
>
> On Thu, Oct 12, 2017 at 10:30 AM, Neuro Lists <
> neuro.mailing.li...@gmail.com> wrote:
>
>> Hi Doug and Bruce,
>> I forgot to mention that I had tried that as well but without success. As
>> a sanity check, tried flipping a label from the 'bert' subject and it still
>> comes out wrong. I've uploaded a screen shot of the result:
>>
>> https://imgur.com/a/J6Phx
>>
>> Thank you for any input you might have!
>>
>> These were the exact steps the following (I also tried playing around
>> with the options to --streg but without luck):
>>
>> cd ${SUBJECTS_DIR}/bert
>> cd surf
>> mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right
>> rh.sphere.left_right
>> cd ../label
>>
>> mris_apply_reg --src-label lh.BA45.label --trg lh_flip.BA45.label --streg
>> ../surf/lh.sphere.left_right ../surf/rh.sphere
>>
>>
>> $Id: mris_apply_reg.c,v 1.9 2016/12/06 19:40:48 greve Exp $
>>
>> cwd /home/joe/subjects/bert/label
>>
>> cmdline ../../scripts/mris_apply_reg --src-label lh.BA45.label --trg
>> lh_flip.BA45.label --streg ../surf/lh.sphere.left_right ../surf/rh.sphere
>>
>> sysname  Linux
>>
>> hostname computer
>>
>> machine  x86_64
>>
>> user joe
>>
>> srcvalfile  (null)
>>
>> trgvalfile  lh_flip.BA45.label
>>
>> nsurfs  2
>>
>> jac  0
>>
>> revmap  0
>>
>> 1 Loading ../surf/lh.sphere.left_right
>>
>> 2 Loading ../surf/rh.sphere
>>
>> Loading label lh.BA45.label
>>
>>4060 points in input label
>>
>> MRISapplyReg: nsurfs = 2, revmap=0, jac=0,  hash=1
>>
>> MRISapplyReg: building hash tables (res=16).
>>
>> MRISapplyReg: Forward Loop (133299)
>>
>> MRISapplyReg: Dividing by number of hits (133299)
>>
>> MRISapplyReg: nSrcLost = 38462
>>
>>4505 points in output label
>>
>> mris_apply_reg done
>>
>>
>>
>>
>>
>> On Thu, Oct 12, 2017 at 5:06 AM, Douglas Greve > > wrote:
>>
>>> Try
>>>
>>> mris_apply_reg --src-label your.lh.label --trg your.rh.label  -streg
>>> lh.sphere.left_right rh.sphere
>>>
>>> On 10/11/17 5:43 PM, Neuro Lists wrote:
>>>
>>> Hi all,
>>> I've searched the lists extensively and have not been able to resolve my
>>> problem. I'd greatly appreciated any help.
>>>
>>> I have run the recon-all pipeline on a number of subjects, made the
>>> appropriate fixes and am happy with the surfaces. For each subject, I have
>>> a number of ROIs that are created programmatically and they are exactly as
>>> they should be. These ROIs are on the "regular" surfaces, not the inflated
>>> ones. In other words, opening the brainmask.mgz in freeview and just
>>> loading the label file results in the ROI being where I expect it to be.
>>>
>>>
>>>  I'm now trying to flip the ROI onto the contralateral hemisphere and
>>> this is going terribly wrong. No matter what I try, the ROI ends up being
>>> generated far outside of the brain.
>>>
>>>
>>> I was originally trying to use the xhemi pipeline, but then I realized
>>> from the forums that I could just use mris_left_right_register.
>>>
>>> I've done:
>>>
>>> cd subject/surf
>>> mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right
>>> rh.sphere.left_right
>>>
>>> I've then tried using a number of varieties of mri_apply_reg that have
>>> been listed on the forum:
>>> 1) mris_apply_reg --src-label your.lh.label --trg your.rh.label  -streg
>>> lh.sphere lh.sphere.left_right
>>> 2) mris_apply_reg --src-label lh.source.label --streg
>>> lh.sphere.left_right
>>> rh.sphere.left_right --trg rh.lh.source.label
>>>
>>>
>>> No matter what I try though, the flipped ROI ends up being way outside
>>> of the brain when I overlay it on the brainmask. Is this because the
>>> flipped ROI should instead be visualized on the inflated hemisphere? If so,
>>> how can I get it to overlay properly onto the brainmask so that I can be
>>> sure it's correct? My ultimate goal is to get anatomical stats from the
>>> original and flipped ROIs.
>>>
>>>
>>> Thanks for your help!
>>>
>>> Joe
>>>
>>>
>>> ___
>>> Freesurfer mailing 
>>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
>>> ___
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>>>
>>>
>>> The information in this e-mail is intended only for the person to whom
>>> it is
>>> addressed. If you believe this e-mail was sent to you 

Re: [Freesurfer] Skull-stripped data submitted on FreeSurfer version 6.0.0

[Douglas N Greve]

Copy it before you run recon-all and copy it to brainmask.mgz (not to 
auto). If there is no brainstem, then I think it will fail


On 10/17/2017 12:55 PM, Duran, Tugce wrote:
> Do you mean after –autorecon1 –noskullstrip done we copy T1.mgz to 
> brainmask.auto.mgz and a link from brainmask.auto.mgz to brainmask.mgz? 
> Because I also did that and saw some cerebral cortex labeled as brain stem. 
> There is no brain-stem in my skull-stripped data.
>
> Tugce
>
>
> dur...@iupui.edu
>
> On 10/17/17, 12:39 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
> Douglas N Greve"  gr...@nmr.mgh.harvard.edu> wrote:
>
>  No, but I think if you copy it to brainmask.mgz that it will then use 
> that
>  
>  
>  On 10/17/2017 12:28 PM, Duran, Tugce wrote:
>  > Is there a flag like –noskullstrip where we can skip brain-stem 
> parcellation/labeling?
>  >
>  > Tugce
>  >
>  > On 10/17/17, 12:07 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on 
> behalf of Douglas N Greve"  of gr...@nmr.mgh.harvard.edu> wrote:
>  >
>  >  if they look ok, then I think they are ok
>  >
>  >
>  >  On 10/17/2017 12:05 PM, Duran, Tugce wrote:
>  >  > That is exaclty right! But how did freesurfer respond to that, 
> performing the skull stripping to skull-stripped data?
>  >  >   Should I trust the results since they looked okay?
>  >  >
>  >  > Tugce
>  >  >
>  >  >
>  >  > dur...@iupui.edu
>  >  >
>  >  > On 10/17/17, 12:00 PM, "freesurfer-boun...@nmr.mgh.harvard.edu 
> on behalf of Douglas N Greve"  behalf of gr...@nmr.mgh.harvard.edu> wrote:
>  >  >
>  >  >  if you put -all AFTER the -noskullstrip, then it would 
> have performed
>  >  >  the skull stripping
>  >  >
>  >  >
>  >  >  On 10/17/2017 10:44 AM, Duran, Tugce wrote:
>  >  >  >
>  >  >  > Dear FreeSurfer Team,
>  >  >  >
>  >  >  > I have recently submitted my skull-stripped data into 
> FreeSurfer v6.
>  >  >  > Since this is a separate process than the default 
> recon-all –all, I
>  >  >  > followed the recommended steps that are posted on the 
> FSwiki website,
>  >  >  > here is the link for it:
>  >  >  > 
> https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.Ihavealreadyskull-strippeddata.CanIsubmitittorecon-all.3F
>  >  >  >
>  >  >  > By doing so, I accidentally submitted my data both with 
> *recon-all
>  >  >  > -autorecon1 -noskullstrip -s  *and *–all *flag 
> at the beginning.
>  >  >  >
>  >  >  > Using PBS script, here is an example of this:
>  >  >  >
>  >  >  > list="E001_V1 E002_V1 E003_V1 E004_V1 E005_V1 E006_V1 
> E008_V1 E010_V1
>  >  >  > E011_V1 E013_V1 E014_V1 E015_V1"
>  >  >  >
>  >  >  > echo $list
>  >  >  >
>  >  >  > OUTDIR="/pathtodirectory/logs_KT"
>  >  >  >
>  >  >  > PREFIX="recon-all"
>  >  >  >
>  >  >  > for index in $list; do
>  >  >  >
>  >  >  > recon-all *–autorecon1 –noskullstrip*-i
>  >  >  > /pathtodirectory/$index/"$index".nii -subject $index -sd
>  >  >  > /pathtodirectory *-all *1>$OUTDIR/$PREFIX.$index.out
>  >  >  > 2>$OUTDIR/$PREFIX.$index.err &
>  >  >  >
>  >  >  > done
>  >  >  >
>  >  >  > wait
>  >  >  >
>  >  >  > I forgot to remove the flag –all at the end of this 
> command.
>  >  >  > Therefore, freesurfer v6 processed my data all the way 
> till the end
>  >  >  > and Viola it worked! And I am wondering If I could trust 
> this data
>  >  >  > since it looks OKAY when I look at the segmentation, 
> parcellation. Can
>  >  >  > I trust this skull-stripped processes data with 
> –autorecon1
>  >  >  > –noskullstrip and –all options?
>  >  >  >
>  >  >  > I hope my explanation and question makes sense.
>  >  >  >
>  >  >  > Thanks,
>  >  >  >
>  >  >  > Tugce Duran
>  >  >  >
>  >  >  > dur...@iupui.edu
>  >  >  >
>  >  >  >
>  >  >  >
>  >  >  > ___
>  >  >  > Freesurfer mailing list
>  >  >  > Freesurfer@nmr.mgh.harvard.edu
>  >  >  > 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>  >  >
>  >  >  --
>  >  >  Douglas N. 

Re: [Freesurfer] Skull-stripped data submitted on FreeSurfer version 6.0.0

[Duran, Tugce]

Do you mean after –autorecon1 –noskullstrip done we copy T1.mgz to 
brainmask.auto.mgz and a link from brainmask.auto.mgz to brainmask.mgz? Because 
I also did that and saw some cerebral cortex labeled as brain stem. There is no 
brain-stem in my skull-stripped data. 

Tugce


dur...@iupui.edu

On 10/17/17, 12:39 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Douglas N Greve"  wrote:

No, but I think if you copy it to brainmask.mgz that it will then use that


On 10/17/2017 12:28 PM, Duran, Tugce wrote:
> Is there a flag like –noskullstrip where we can skip brain-stem 
parcellation/labeling?
>
> Tugce
>
> On 10/17/17, 12:07 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf 
of Douglas N Greve"  wrote:
>
>  if they look ok, then I think they are ok
>  
>  
>  On 10/17/2017 12:05 PM, Duran, Tugce wrote:
>  > That is exaclty right! But how did freesurfer respond to that, 
performing the skull stripping to skull-stripped data?
>  >   Should I trust the results since they looked okay?
>  >
>  > Tugce
>  >
>  >
>  > dur...@iupui.edu
>  >
>  > On 10/17/17, 12:00 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on 
behalf of Douglas N Greve"  wrote:
>  >
>  >  if you put -all AFTER the -noskullstrip, then it would have 
performed
>  >  the skull stripping
>  >
>  >
>  >  On 10/17/2017 10:44 AM, Duran, Tugce wrote:
>  >  >
>  >  > Dear FreeSurfer Team,
>  >  >
>  >  > I have recently submitted my skull-stripped data into 
FreeSurfer v6.
>  >  > Since this is a separate process than the default recon-all 
–all, I
>  >  > followed the recommended steps that are posted on the 
FSwiki website,
>  >  > here is the link for it:
>  >  > 
https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.Ihavealreadyskull-strippeddata.CanIsubmitittorecon-all.3F
>  >  >
>  >  > By doing so, I accidentally submitted my data both with 
*recon-all
>  >  > -autorecon1 -noskullstrip -s  *and *–all *flag at 
the beginning.
>  >  >
>  >  > Using PBS script, here is an example of this:
>  >  >
>  >  > list="E001_V1 E002_V1 E003_V1 E004_V1 E005_V1 E006_V1 
E008_V1 E010_V1
>  >  > E011_V1 E013_V1 E014_V1 E015_V1"
>  >  >
>  >  > echo $list
>  >  >
>  >  > OUTDIR="/pathtodirectory/logs_KT"
>  >  >
>  >  > PREFIX="recon-all"
>  >  >
>  >  > for index in $list; do
>  >  >
>  >  > recon-all *–autorecon1 –noskullstrip*-i
>  >  > /pathtodirectory/$index/"$index".nii -subject $index -sd
>  >  > /pathtodirectory *-all *1>$OUTDIR/$PREFIX.$index.out
>  >  > 2>$OUTDIR/$PREFIX.$index.err &
>  >  >
>  >  > done
>  >  >
>  >  > wait
>  >  >
>  >  > I forgot to remove the flag –all at the end of this command.
>  >  > Therefore, freesurfer v6 processed my data all the way till 
the end
>  >  > and Viola it worked! And I am wondering If I could trust 
this data
>  >  > since it looks OKAY when I look at the segmentation, 
parcellation. Can
>  >  > I trust this skull-stripped processes data with –autorecon1
>  >  > –noskullstrip and –all options?
>  >  >
>  >  > I hope my explanation and question makes sense.
>  >  >
>  >  > Thanks,
>  >  >
>  >  > Tugce Duran
>  >  >
>  >  > dur...@iupui.edu
>  >  >
>  >  >
>  >  >
>  >  > ___
>  >  > Freesurfer mailing list
>  >  > Freesurfer@nmr.mgh.harvard.edu
>  >  > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>  >
>  >  --
>  >  Douglas N. Greve, Ph.D.
>  >  MGH-NMR Center
>  >  gr...@nmr.mgh.harvard.edu
>  >  Phone Number: 617-724-2358
>  >  Fax: 617-726-7422
>  >
>  >  Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>  >  FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>  >  www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>  >  Outgoing: 
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> 

Re: [Freesurfer] Skull-stripped data submitted on FreeSurfer version 6.0.0

[Douglas N Greve]

No, but I think if you copy it to brainmask.mgz that it will then use that


On 10/17/2017 12:28 PM, Duran, Tugce wrote:
> Is there a flag like –noskullstrip where we can skip brain-stem 
> parcellation/labeling?
>
> Tugce
>
> On 10/17/17, 12:07 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
> Douglas N Greve"  gr...@nmr.mgh.harvard.edu> wrote:
>
>  if they look ok, then I think they are ok
>  
>  
>  On 10/17/2017 12:05 PM, Duran, Tugce wrote:
>  > That is exaclty right! But how did freesurfer respond to that, 
> performing the skull stripping to skull-stripped data?
>  >   Should I trust the results since they looked okay?
>  >
>  > Tugce
>  >
>  >
>  > dur...@iupui.edu
>  >
>  > On 10/17/17, 12:00 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on 
> behalf of Douglas N Greve"  of gr...@nmr.mgh.harvard.edu> wrote:
>  >
>  >  if you put -all AFTER the -noskullstrip, then it would have 
> performed
>  >  the skull stripping
>  >
>  >
>  >  On 10/17/2017 10:44 AM, Duran, Tugce wrote:
>  >  >
>  >  > Dear FreeSurfer Team,
>  >  >
>  >  > I have recently submitted my skull-stripped data into 
> FreeSurfer v6.
>  >  > Since this is a separate process than the default recon-all 
> –all, I
>  >  > followed the recommended steps that are posted on the FSwiki 
> website,
>  >  > here is the link for it:
>  >  > 
> https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.Ihavealreadyskull-strippeddata.CanIsubmitittorecon-all.3F
>  >  >
>  >  > By doing so, I accidentally submitted my data both with 
> *recon-all
>  >  > -autorecon1 -noskullstrip -s  *and *–all *flag at the 
> beginning.
>  >  >
>  >  > Using PBS script, here is an example of this:
>  >  >
>  >  > list="E001_V1 E002_V1 E003_V1 E004_V1 E005_V1 E006_V1 E008_V1 
> E010_V1
>  >  > E011_V1 E013_V1 E014_V1 E015_V1"
>  >  >
>  >  > echo $list
>  >  >
>  >  > OUTDIR="/pathtodirectory/logs_KT"
>  >  >
>  >  > PREFIX="recon-all"
>  >  >
>  >  > for index in $list; do
>  >  >
>  >  > recon-all *–autorecon1 –noskullstrip*-i
>  >  > /pathtodirectory/$index/"$index".nii -subject $index -sd
>  >  > /pathtodirectory *-all *1>$OUTDIR/$PREFIX.$index.out
>  >  > 2>$OUTDIR/$PREFIX.$index.err &
>  >  >
>  >  > done
>  >  >
>  >  > wait
>  >  >
>  >  > I forgot to remove the flag –all at the end of this command.
>  >  > Therefore, freesurfer v6 processed my data all the way till the 
> end
>  >  > and Viola it worked! And I am wondering If I could trust this 
> data
>  >  > since it looks OKAY when I look at the segmentation, 
> parcellation. Can
>  >  > I trust this skull-stripped processes data with –autorecon1
>  >  > –noskullstrip and –all options?
>  >  >
>  >  > I hope my explanation and question makes sense.
>  >  >
>  >  > Thanks,
>  >  >
>  >  > Tugce Duran
>  >  >
>  >  > dur...@iupui.edu
>  >  >
>  >  >
>  >  >
>  >  > ___
>  >  > Freesurfer mailing list
>  >  > Freesurfer@nmr.mgh.harvard.edu
>  >  > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>  >
>  >  --
>  >  Douglas N. Greve, Ph.D.
>  >  MGH-NMR Center
>  >  gr...@nmr.mgh.harvard.edu
>  >  Phone Number: 617-724-2358
>  >  Fax: 617-726-7422
>  >
>  >  Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>  >  FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>  >  www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>  >  Outgoing: 
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>  >
>  >  ___
>  >  Freesurfer mailing list
>  >  Freesurfer@nmr.mgh.harvard.edu
>  >  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>  >
>  >
>  >  The information in this e-mail is intended only for the person to 
> whom it is
>  >  addressed. If you believe this e-mail was sent to you in error 
> and the e-mail
>  >  contains patient information, please contact the Partners 
> Compliance HelpLine at
>  >  http://www.partners.org/complianceline . If the e-mail was sent 
> to you in error
>  >  but does not contain patient information, please contact the 
> sender and properly
>  >  dispose of the e-mail.
>  >
>  >
>  >
>  > 

Re: [Freesurfer] Skull-stripped data submitted on FreeSurfer version 6.0.0

[Duran, Tugce]

Is there a flag like –noskullstrip where we can skip brain-stem 
parcellation/labeling? 

Tugce

On 10/17/17, 12:07 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Douglas N Greve"  wrote:

if they look ok, then I think they are ok


On 10/17/2017 12:05 PM, Duran, Tugce wrote:
> That is exaclty right! But how did freesurfer respond to that, performing 
the skull stripping to skull-stripped data?
>   Should I trust the results since they looked okay?
>
> Tugce
>
>
> dur...@iupui.edu
>
> On 10/17/17, 12:00 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf 
of Douglas N Greve"  wrote:
>
>  if you put -all AFTER the -noskullstrip, then it would have performed
>  the skull stripping
>  
>  
>  On 10/17/2017 10:44 AM, Duran, Tugce wrote:
>  >
>  > Dear FreeSurfer Team,
>  >
>  > I have recently submitted my skull-stripped data into FreeSurfer 
v6.
>  > Since this is a separate process than the default recon-all –all, I
>  > followed the recommended steps that are posted on the FSwiki 
website,
>  > here is the link for it:
>  > 
https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.Ihavealreadyskull-strippeddata.CanIsubmitittorecon-all.3F
>  >
>  > By doing so, I accidentally submitted my data both with *recon-all
>  > -autorecon1 -noskullstrip -s  *and *–all *flag at the 
beginning.
>  >
>  > Using PBS script, here is an example of this:
>  >
>  > list="E001_V1 E002_V1 E003_V1 E004_V1 E005_V1 E006_V1 E008_V1 
E010_V1
>  > E011_V1 E013_V1 E014_V1 E015_V1"
>  >
>  > echo $list
>  >
>  > OUTDIR="/pathtodirectory/logs_KT"
>  >
>  > PREFIX="recon-all"
>  >
>  > for index in $list; do
>  >
>  > recon-all *–autorecon1 –noskullstrip*-i
>  > /pathtodirectory/$index/"$index".nii -subject $index -sd
>  > /pathtodirectory *-all *1>$OUTDIR/$PREFIX.$index.out
>  > 2>$OUTDIR/$PREFIX.$index.err &
>  >
>  > done
>  >
>  > wait
>  >
>  > I forgot to remove the flag –all at the end of this command.
>  > Therefore, freesurfer v6 processed my data all the way till the end
>  > and Viola it worked! And I am wondering If I could trust this data
>  > since it looks OKAY when I look at the segmentation, parcellation. 
Can
>  > I trust this skull-stripped processes data with –autorecon1
>  > –noskullstrip and –all options?
>  >
>  > I hope my explanation and question makes sense.
>  >
>  > Thanks,
>  >
>  > Tugce Duran
>  >
>  > dur...@iupui.edu
>  >
>  >
>  >
>  > ___
>  > Freesurfer mailing list
>  > Freesurfer@nmr.mgh.harvard.edu
>  > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>  
>  --
>  Douglas N. Greve, Ph.D.
>  MGH-NMR Center
>  gr...@nmr.mgh.harvard.edu
>  Phone Number: 617-724-2358
>  Fax: 617-726-7422
>  
>  Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>  FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>  www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>  Outgoing: 
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>  
>  ___
>  Freesurfer mailing list
>  Freesurfer@nmr.mgh.harvard.edu
>  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>  
>  
>  The information in this e-mail is intended only for the person to 
whom it is
>  addressed. If you believe this e-mail was sent to you in error and 
the e-mail
>  contains patient information, please contact the Partners Compliance 
HelpLine at
>  http://www.partners.org/complianceline . If the e-mail was sent to 
you in error
>  but does not contain patient information, please contact the sender 
and properly
>  dispose of the e-mail.
>  
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2

Re: [Freesurfer] lta_convert does not produce ITK transforms that are correctly applied by antsApplyTransforms

[Christopher Markiewicz]

Hi Martin,

I've uploaded a .tgz file with a T1w volume, BOLD volume, and a valid LTA file.

https://gate.nmr.mgh.harvard.edu/filedrop2/?g=7f71pykmv7p

Chris

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Martin Reuter 

Sent: Tuesday, October 17, 2017 9:32:54 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] lta_convert does not produce ITK transforms that are 
correctly applied by antsApplyTransforms

Hi Chris,

thanks, can you send the images and the exact commands. We have had success in 
the past, could be that you have a special case (e.g. maybe we never tested 
registration across different resolutions or whatever?).

Thanks, Martin

https://gate.nmr.mgh.harvard.edu/filedrop2/


On 16. Oct 2017, at 19:37, Christopher Markiewicz 
> wrote:

Doug,

Sorry if I muddied things by going into the significant digits - accurate to 5 
seems reasonable. I was simply meaning to say that the rotation and scaling 
parameters are not the issue, to save the reader time inspecting them.

The translations (final three parameters) are off by anywhere 3 to 54mm, though.

LTA-FSL-ITK: 1.3066136395454464 -45.60342165876236 -43.10584860730749
LTA-ITK: -2.2848172187805176 -2.9065067768096924 11.744022369384766

I'm guessing lta_convert has the wrong model of the origin in ITK style 
affines, at least as applied by antsApplyTransforms.

Chris

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
>
 on behalf of Douglas Greve 
>
Sent: Monday, October 16, 2017 12:39:28 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] lta_convert does not produce ITK transforms that are 
correctly applied by antsApplyTransforms

Not sure I understand. If the two transforms are only off by less than
the 5th decimal, then why are the registrations off so much. As for why
it would be off at the 5ht dec, it probably has to do with the way we
store the matrix. When a volume is read in, the matrix is decomposed
into translation, scale, and direction cosine, and then the matrix is
thrown away. When a volume with the same geometry is written out, the
matrix is recomputed. Some resolution is lost during the
decomposition/recomposition, and we don't end up with the exact same matrix.


On 10/14/17 1:30 PM, Christopher Markiewicz wrote:
Hi,

I've used `bbregister` to generate a transform `bold2T1.lta` from `bold.nii` to 
`T1.mgz` (assume we have a `T1.nii` as well for the sake of ANTs).

The following produces a well-aligned output:

mri_convert --apply_transform bold2T1.lta bold.nii bold_space-T1.nii

As does the following:

lta_convert --inlta bold2T1.lta --outfsl bold2T1.mat
c3d_affine_tool -ref T1.nii -src bold.nii bold2T1.mat -fsl2ras -oitk 
bold2T1.txt
antsApplyTransforms -i bold.nii -r T1.nii -o bold_space-T1.nii -t 
bold2T1.txt

However, if one skips the FSL step, the registration is quite far off:

lta_convert --inlta bold2T1.lta --outitk bold2T1.txt
antsApplyTransforms -i bold.nii -r T1.nii -o bold_space-T1.nii -t 
bold2T1.txt

Comparing the ITK transform files:

LTA-FSL-ITK

#Insight Transform File V1.0
#Transform 0
Transform: MatrixOffsetTransformBase_double_3_3
Parameters: 0.9895096215486424 0.011126830936108464 -0.00042204653562094823 
-0.01079971161879626 0.872329255299452 -0.42602926756857834 
-0.004755964529051335 0.42420535065804454 0.8878552541301569 
-1.3066136395454464 -45.60342165876236 -43.10584860730749
FixedParameters: 0 0 0


LTA-ITK

#Insight Transform File V1.0
#Transform 0
Transform: AffineTransform_double_3_3
Parameters: 0.98950976133346558 0.011126830242574215 
-0.00042204943019896746 -0.010799713432788849 0.87232941389083862 
-0.42602935433387756 -0.0047559700906276703 0.42420542240142822 
0.88785547018051147 -2.2848172187805176 -2.9065067768096924 11.744022369384766
FixedParameters: 0 0 0


To 5 significant digits, these are the same, except the last three 
(translation) parameters. And the `AffineTransform_double_3_3` is different 
from `MatrixOffsetTransformBase_double_3_3`, though I'm not sure whether this 
has any effect.

Here is the original LTA:

type  = 1 # LINEAR_RAS_TO_RAS
nxforms   = 1
mean  = 0. 0. 0.
sigma = 1.
1 4 4
1.010462999343872e+00 -1.063966564834118e-02 4.625014495104551e-03 
-2.332115173339844e+00
1.228639855980873e-02 9.293417930603027e-01 -4.459420144557953e-01 
2.507942199707031e+00
4.575361963361502e-04 4.440840482711792e-01 9.132194519042969e-01 
-1.201664733886719e+01
0.000e+00 

Re: [Freesurfer] Skull-stripped data submitted on FreeSurfer version 6.0.0

[Douglas N Greve]

if they look ok, then I think they are ok


On 10/17/2017 12:05 PM, Duran, Tugce wrote:
> That is exaclty right! But how did freesurfer respond to that, performing the 
> skull stripping to skull-stripped data?
>   Should I trust the results since they looked okay?
>
> Tugce
>
>
> dur...@iupui.edu
>
> On 10/17/17, 12:00 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
> Douglas N Greve"  gr...@nmr.mgh.harvard.edu> wrote:
>
>  if you put -all AFTER the -noskullstrip, then it would have performed
>  the skull stripping
>  
>  
>  On 10/17/2017 10:44 AM, Duran, Tugce wrote:
>  >
>  > Dear FreeSurfer Team,
>  >
>  > I have recently submitted my skull-stripped data into FreeSurfer v6.
>  > Since this is a separate process than the default recon-all –all, I
>  > followed the recommended steps that are posted on the FSwiki website,
>  > here is the link for it:
>  > 
> https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.Ihavealreadyskull-strippeddata.CanIsubmitittorecon-all.3F
>  >
>  > By doing so, I accidentally submitted my data both with *recon-all
>  > -autorecon1 -noskullstrip -s  *and *–all *flag at the 
> beginning.
>  >
>  > Using PBS script, here is an example of this:
>  >
>  > list="E001_V1 E002_V1 E003_V1 E004_V1 E005_V1 E006_V1 E008_V1 E010_V1
>  > E011_V1 E013_V1 E014_V1 E015_V1"
>  >
>  > echo $list
>  >
>  > OUTDIR="/pathtodirectory/logs_KT"
>  >
>  > PREFIX="recon-all"
>  >
>  > for index in $list; do
>  >
>  > recon-all *–autorecon1 –noskullstrip*-i
>  > /pathtodirectory/$index/"$index".nii -subject $index -sd
>  > /pathtodirectory *-all *1>$OUTDIR/$PREFIX.$index.out
>  > 2>$OUTDIR/$PREFIX.$index.err &
>  >
>  > done
>  >
>  > wait
>  >
>  > I forgot to remove the flag –all at the end of this command.
>  > Therefore, freesurfer v6 processed my data all the way till the end
>  > and Viola it worked! And I am wondering If I could trust this data
>  > since it looks OKAY when I look at the segmentation, parcellation. Can
>  > I trust this skull-stripped processes data with –autorecon1
>  > –noskullstrip and –all options?
>  >
>  > I hope my explanation and question makes sense.
>  >
>  > Thanks,
>  >
>  > Tugce Duran
>  >
>  > dur...@iupui.edu
>  >
>  >
>  >
>  > ___
>  > Freesurfer mailing list
>  > Freesurfer@nmr.mgh.harvard.edu
>  > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>  
>  --
>  Douglas N. Greve, Ph.D.
>  MGH-NMR Center
>  gr...@nmr.mgh.harvard.edu
>  Phone Number: 617-724-2358
>  Fax: 617-726-7422
>  
>  Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>  FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>  www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>  Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>  
>  ___
>  Freesurfer mailing list
>  Freesurfer@nmr.mgh.harvard.edu
>  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>  
>  
>  The information in this e-mail is intended only for the person to whom 
> it is
>  addressed. If you believe this e-mail was sent to you in error and the 
> e-mail
>  contains patient information, please contact the Partners Compliance 
> HelpLine at
>  http://www.partners.org/complianceline . If the e-mail was sent to you 
> in error
>  but does not contain patient information, please contact the sender and 
> properly
>  dispose of the e-mail.
>  
>
>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] Skull-stripped data submitted on FreeSurfer version 6.0.0

[Duran, Tugce]

That is exaclty right! But how did freesurfer respond to that, performing the 
skull stripping to skull-stripped data?
 Should I trust the results since they looked okay?

Tugce


dur...@iupui.edu

On 10/17/17, 12:00 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Douglas N Greve"  wrote:

if you put -all AFTER the -noskullstrip, then it would have performed 
the skull stripping


On 10/17/2017 10:44 AM, Duran, Tugce wrote:
>
> Dear FreeSurfer Team,
>
> I have recently submitted my skull-stripped data into FreeSurfer v6. 
> Since this is a separate process than the default recon-all –all, I 
> followed the recommended steps that are posted on the FSwiki website, 
> here is the link for it: 
> 
https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.Ihavealreadyskull-strippeddata.CanIsubmitittorecon-all.3F
>
> By doing so, I accidentally submitted my data both with *recon-all 
> -autorecon1 -noskullstrip -s  *and *–all *flag at the beginning.
>
> Using PBS script, here is an example of this:
>
> list="E001_V1 E002_V1 E003_V1 E004_V1 E005_V1 E006_V1 E008_V1 E010_V1 
> E011_V1 E013_V1 E014_V1 E015_V1"
>
> echo $list
>
> OUTDIR="/pathtodirectory/logs_KT"
>
> PREFIX="recon-all"
>
> for index in $list; do
>
> recon-all *–autorecon1 –noskullstrip*-i 
> /pathtodirectory/$index/"$index".nii -subject $index -sd 
> /pathtodirectory *-all *1>$OUTDIR/$PREFIX.$index.out 
> 2>$OUTDIR/$PREFIX.$index.err &
>
> done
>
> wait
>
> I forgot to remove the flag –all at the end of this command. 
> Therefore, freesurfer v6 processed my data all the way till the end 
> and Viola it worked! And I am wondering If I could trust this data 
> since it looks OKAY when I look at the segmentation, parcellation. Can 
> I trust this skull-stripped processes data with –autorecon1 
> –noskullstrip and –all options?
>
> I hope my explanation and question makes sense.
>
> Thanks,
>
> Tugce Duran
>
> dur...@iupui.edu
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the 
e-mail
contains patient information, please contact the Partners Compliance 
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in 
error
but does not contain patient information, please contact the sender and 
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Re: [Freesurfer] Skull-stripped data submitted on FreeSurfer version 6.0.0

[Douglas N Greve]

if you put -all AFTER the -noskullstrip, then it would have performed 
the skull stripping


On 10/17/2017 10:44 AM, Duran, Tugce wrote:
>
> Dear FreeSurfer Team,
>
> I have recently submitted my skull-stripped data into FreeSurfer v6. 
> Since this is a separate process than the default recon-all –all, I 
> followed the recommended steps that are posted on the FSwiki website, 
> here is the link for it: 
> https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.Ihavealreadyskull-strippeddata.CanIsubmitittorecon-all.3F
>
> By doing so, I accidentally submitted my data both with *recon-all 
> -autorecon1 -noskullstrip -s  *and *–all *flag at the beginning.
>
> Using PBS script, here is an example of this:
>
> list="E001_V1 E002_V1 E003_V1 E004_V1 E005_V1 E006_V1 E008_V1 E010_V1 
> E011_V1 E013_V1 E014_V1 E015_V1"
>
> echo $list
>
> OUTDIR="/pathtodirectory/logs_KT"
>
> PREFIX="recon-all"
>
> for index in $list; do
>
> recon-all *–autorecon1 –noskullstrip*-i 
> /pathtodirectory/$index/"$index".nii -subject $index -sd 
> /pathtodirectory *-all *1>$OUTDIR/$PREFIX.$index.out 
> 2>$OUTDIR/$PREFIX.$index.err &
>
> done
>
> wait
>
> I forgot to remove the flag –all at the end of this command. 
> Therefore, freesurfer v6 processed my data all the way till the end 
> and Viola it worked! And I am wondering If I could trust this data 
> since it looks OKAY when I look at the segmentation, parcellation. Can 
> I trust this skull-stripped processes data with –autorecon1 
> –noskullstrip and –all options?
>
> I hope my explanation and question makes sense.
>
> Thanks,
>
> Tugce Duran
>
> dur...@iupui.edu
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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[Freesurfer] Fwd: cortical/subcortical volume based analysis

[miracle ozzoude]

-- Forwarded message --
From: miracle ozzoude 
Date: Sat, Oct 14, 2017 at 3:32 PM
Subject: Re: [Freesurfer] cortical/subcortical volume based analysis
To: Freesurfer support list 


Hello Bruce,

Thank you for the response. I was able to look into CVS command and I wrote
a command on how to register each subjects to cvs_avg35_inMNI152 template
using the following: mri_cvs_register --mov subID --mni
/Application/freesurfer/subjects/cvs_avg35_inMNI152/T1.mgz --step1 --step2
--step3 --outdir  $SUBJECTS_DIR/$subID/cvs  --asegfname aparc+aseg --openmp
8. Do i need to use the T1 in the mri folder or mri.2mm folder when
performing mri_cvs_register?

My next goals are to:
1) sample the volumes created using mri_cvs_register to the
cvs_avg35_inMNI152 template using mri_vol2vol -reg .
-which of the outputs from mri_cvs_register should i use to achieve?
final_CVSmorphed_toTEMPLATE_norm.mgz,final_CVSmorph_toTEMPLATE.m3z, or
final_CVSmorphed_toTEMPLATE_aseg.mgz

2)Use a cortical+subcortical mask from cvs_avg35_inMNI152 to smooth the
output from mri_vol2vol.
  - How can I create the cortical mask from the
cvs_avg35_inMNI152/mri.2mm folder? This is because the folder already has a
subcortical mask and I want to create a cortical mask, combine both (using
mri_merge) and use it to smooth with 8mm.

3) Lastly, use mri_concat to combine the smoothened maps in order to
perform group level analysis on them.
  - when performing mri_glmfit on the combined maps, i don't need to
specify the --surf fsaverage and lh/rh flags because it is a volume based
analysis and it was done on MNI template not fsaverage?

Thank you very much

Best,
Paul


On Sat, Oct 14, 2017 at 12:38 PM, Bruce Fischl 
wrote:

> Hi Paul
>
> I guess you could use CVS for this.
>
> cheers
> Bruce
>
> On Sat, 14 Oct 2017, miracle ozzoude wrote:
>
> Hello Bruce,
>>
>> Thank you very much. Can I still general cortical and subcortical maps
>> with the Spherical warp of r/lh.white surface?  If yes, please what are the
>> steps to achieve this? can I still analyze it with mri_glm?
>>
>> Best,
>> Paul
>>
>> Sent from my BlackBerry 10 smartphone.
>>   Original Message
>> From: Bruce Fischl
>> Sent: Saturday, October 14, 2017 11:27 AM
>> To: Freesurfer support list
>> Reply To: Freesurfer support list
>> Subject: Re: [Freesurfer] cortical/subcortical volume based analysis
>>
>> Hi Paul
>>
>> if you use a property (like gm) to drive intersubject registration it then
>> becomes difficult to also analyze it. If your warp was truly perfect you
>> could just analyze the properties of the warp, but even then it is hard to
>> localize effects (e.g. if you changed the smoothness of the warp field
>> would the effect move somewhere else?). If the warp is not perfect then
>> some of the effect is in your warp and some in the residual anatomical
>> differences. There are lots of caveats like this you have to worry about.
>> It's the reason we drive our spherical warp with the ?h.white surface. It
>> is invariant to gm atrophy and so can be used to assess it without
>> worrying
>> about this kind of thing
>>
>> cheers
>> Bruce
>>
>>
>>
>> On Fri, 13 Oct 2017, miracle ozzoude wrote:
>>
>> Hello Bruce,
>>>
>>> Thank you for the response. I meant the latter ( making maps etc). I
>>> want to do something similar to the subcortical volume based analysis on
>>> PETSurfer page however, on freesurfer T1. Freesurfer doesn't perform VBM
>>> hence, why should there be a problem with interpretation?
>>>
>>> Best,
>>> Miracle
>>>
>>> Sent from my BlackBerry 10 smartphone.
>>>   Original Message
>>> From: Bruce Fischl
>>> Sent: Friday, October 13, 2017 6:53 PM
>>> To: Freesurfer support list
>>> Reply To: Freesurfer support list
>>> Subject: Re: [Freesurfer] cortical/subcortical volume based analysis
>>>
>>> Hi Paul
>>>
>>> we typically do this type of analysis by looking at scatter plots of
>>> structure volumes (e.g. hippocampus). Alternatively, you can make maps,
>>> but that opens up all the problems/difficulties of interpretation of VBM.
>>> Which did you mean?
>>> cheers
>>> Bruce
>>>
>>> On Fri, 13 Oct 2017, miracle ozzoude wrote:
>>>
>>> Hello FreeSurfer experts,
 I want to perform a whole brain volume based group analysis for
 cortical and subcortical regions.
 That's something very similar to surface based group analysis for
 cortical thickness however, for
 volume. Is there a tutorial on how to do it? if yes, please can i get
 the link. If not, please can
 someone direct me how to go about doing it? My goal is to perform a
 group comparison between control
 and PD patients based on volume. Thank you very much.

 Best,
 Paul



>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
>>>

[Freesurfer] Fwd: running cross sectional analysis on .long outputs only

[Garret O'Connell]

Hello FreeSurfer experts,

I am trying to do a cross-sectional baseline analysis from the outputs of
the longitudinal processing stream, following the advice on a previous
question's thread:

https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-
March/044681.html

>From my reading of the issue, I need to run the following command, entering
the cross-sectional title folder as the first input.

recon-all -long "subj_crossfolder" "subj_base" -qcache

For this step, i know it is necessary that recon-all knows where the cross
folders are located, although from my understanding, it does not actually
use data from these folders., instead using the data in the .long folders.

My issue is that I do not have access to the cross folders anymore, and was
wondering if there was a work around to do the cross sectional analysis
without them?

Thanks for any help!
Garret
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[Freesurfer] Skull-stripped data submitted on FreeSurfer version 6.0.0

[Duran, Tugce]

Dear FreeSurfer Team,

I have recently submitted my skull-stripped data into FreeSurfer v6. Since this 
is a separate process than the default recon-all –all, I followed the 
recommended steps that are posted on the FSwiki website, here is the link for 
it: 
https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.Ihavealreadyskull-strippeddata.CanIsubmitittorecon-all.3F

By doing so, I accidentally submitted my data both with recon-all -autorecon1 
-noskullstrip -s  and –all flag at the beginning.
Using PBS script, here is an example of this:

list="E001_V1 E002_V1 E003_V1 E004_V1 E005_V1 E006_V1 E008_V1 E010_V1 E011_V1 
E013_V1 E014_V1 E015_V1"
echo $list
OUTDIR="/pathtodirectory/logs_KT"
PREFIX="recon-all"

for index in $list; do
recon-all –autorecon1 –noskullstrip -i /pathtodirectory/$index/"$index".nii 
-subject $index -sd /pathtodirectory -all 1>$OUTDIR/$PREFIX.$index.out 
2>$OUTDIR/$PREFIX.$index.err &
done
wait
I forgot to remove the flag –all at the end of this command. Therefore, 
freesurfer v6 processed my data all the way till the end and Viola it worked! 
And I am wondering If I could trust this data since it looks OKAY when I look 
at the segmentation, parcellation. Can I trust this skull-stripped processes 
data with –autorecon1 –noskullstrip and –all options?
I hope my explanation and question makes sense.

Thanks,
Tugce Duran
dur...@iupui.edu

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Re: [Freesurfer] lta_convert does not produce ITK transforms that are correctly applied by antsApplyTransforms

[Martin Reuter]

Hi Chris, 

thanks, can you send the images and the exact commands. We have had success in 
the past, could be that you have a special case (e.g. maybe we never tested 
registration across different resolutions or whatever?).

Thanks, Martin

https://gate.nmr.mgh.harvard.edu/filedrop2/ 
 


> On 16. Oct 2017, at 19:37, Christopher Markiewicz  
> wrote:
> 
> Doug,
> 
> Sorry if I muddied things by going into the significant digits - accurate to 
> 5 seems reasonable. I was simply meaning to say that the rotation and scaling 
> parameters are not the issue, to save the reader time inspecting them.
> 
> The translations (final three parameters) are off by anywhere 3 to 54mm, 
> though.
> 
> LTA-FSL-ITK: 1.3066136395454464 -45.60342165876236 -43.10584860730749
> LTA-ITK: -2.2848172187805176 -2.9065067768096924 11.744022369384766
> 
> I'm guessing lta_convert has the wrong model of the origin in ITK style 
> affines, at least as applied by antsApplyTransforms.
> 
> Chris
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas Greve 
> 
> Sent: Monday, October 16, 2017 12:39:28 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] lta_convert does not produce ITK transforms that 
> are correctly applied by antsApplyTransforms
> 
> Not sure I understand. If the two transforms are only off by less than
> the 5th decimal, then why are the registrations off so much. As for why
> it would be off at the 5ht dec, it probably has to do with the way we
> store the matrix. When a volume is read in, the matrix is decomposed
> into translation, scale, and direction cosine, and then the matrix is
> thrown away. When a volume with the same geometry is written out, the
> matrix is recomputed. Some resolution is lost during the
> decomposition/recomposition, and we don't end up with the exact same matrix.
> 
> 
> On 10/14/17 1:30 PM, Christopher Markiewicz wrote:
>> Hi,
>> 
>> I've used `bbregister` to generate a transform `bold2T1.lta` from `bold.nii` 
>> to `T1.mgz` (assume we have a `T1.nii` as well for the sake of ANTs).
>> 
>> The following produces a well-aligned output:
>> 
>> mri_convert --apply_transform bold2T1.lta bold.nii bold_space-T1.nii
>> 
>> As does the following:
>> 
>> lta_convert --inlta bold2T1.lta --outfsl bold2T1.mat
>> c3d_affine_tool -ref T1.nii -src bold.nii bold2T1.mat -fsl2ras -oitk 
>> bold2T1.txt
>> antsApplyTransforms -i bold.nii -r T1.nii -o bold_space-T1.nii -t 
>> bold2T1.txt
>> 
>> However, if one skips the FSL step, the registration is quite far off:
>> 
>> lta_convert --inlta bold2T1.lta --outitk bold2T1.txt
>> antsApplyTransforms -i bold.nii -r T1.nii -o bold_space-T1.nii -t 
>> bold2T1.txt
>> 
>> Comparing the ITK transform files:
>> 
>> LTA-FSL-ITK
>> 
>> #Insight Transform File V1.0
>> #Transform 0
>> Transform: MatrixOffsetTransformBase_double_3_3
>> Parameters: 0.9895096215486424 0.011126830936108464 
>> -0.00042204653562094823 -0.01079971161879626 0.872329255299452 
>> -0.42602926756857834 -0.004755964529051335 0.42420535065804454 
>> 0.8878552541301569 -1.3066136395454464 -45.60342165876236 -43.10584860730749
>> FixedParameters: 0 0 0
>> 
>> 
>> LTA-ITK
>> 
>> #Insight Transform File V1.0
>> #Transform 0
>> Transform: AffineTransform_double_3_3
>> Parameters: 0.98950976133346558 0.011126830242574215 
>> -0.00042204943019896746 -0.010799713432788849 0.87232941389083862 
>> -0.42602935433387756 -0.0047559700906276703 0.42420542240142822 
>> 0.88785547018051147 -2.2848172187805176 -2.9065067768096924 
>> 11.744022369384766
>> FixedParameters: 0 0 0
>> 
>> 
>> To 5 significant digits, these are the same, except the last three 
>> (translation) parameters. And the `AffineTransform_double_3_3` is different 
>> from `MatrixOffsetTransformBase_double_3_3`, though I'm not sure whether 
>> this has any effect.
>> 
>> Here is the original LTA:
>> 
>> type  = 1 # LINEAR_RAS_TO_RAS
>> nxforms   = 1
>> mean  = 0. 0. 0.
>> sigma = 1.
>> 1 4 4
>> 1.010462999343872e+00 -1.063966564834118e-02 4.625014495104551e-03 
>> -2.332115173339844e+00
>> 1.228639855980873e-02 9.293417930603027e-01 -4.459420144557953e-01 
>> 2.507942199707031e+00
>> 4.575361963361502e-04 4.440840482711792e-01 9.132194519042969e-01 
>> -1.201664733886719e+01
>> 0.000e+00 0.000e+00 0.000e+00 
>> 9.98807907104e-01
>> src volume info
>> valid = 1  # volume info valid
>> filename = 
>> /scratch/fmriprep_wf/single_subject_02_wf/func_preproc_task_short_wf/bold_reg_wf/bbreg_wf/bbregister/uni_masked_xform.nii.gz
>> volume = 64 64 34
>> voxelsize = 3.125e+00 3.125e+00 
>> 4.000e+00
>> xras   = 

[Freesurfer] Selecting OS for image analysis

[Ramesh Babu]

Dear Experts,
I have purchased a new pc. I want to use for MRI and EEG analysis by using
MATLAB, FSL, SPM, Fresurfer etc,. Which OS is suitable to handle these
software?
I have NVIDIA graphics card 610 in my system.

I am using Ubuntu in another systm and little bit of experience in cent os.


Thank in advance
Ramesh
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